From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Dec 20 2006 - 10:13:41 CST
> I've blindly implemented this in my TCLForces code but I'd be grateful if someone could tell me I'm thinking along the right lines - in particular I was surprised that the force applied is in fact linearly proportional to the distance from reference co-ordinates, whereas the energy scales by r^2... or am I missing something?
It's just a harmonic force; this isn't different from any other spring.
Would you expect something else?
> And most importantly for my purposes, will the reported energy be comparable, (in the same units etc), with the rest of the system energy?
>
Your approach sounds reasonable, so as long as you're using the same
constants and units you should get the same answer (since you're doing
the exact same calculation ;-). You'll need to check on the units for
the constant though; I believe namd keeps its internal distance units in
angstroms.
> Thanks a lot!
>
> Floris Buelens
> Department of Crystallography, Birkbeck College, London
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